Beta thalassemia: genes and variants
Beta thalassemia is linked to 1 analyzed protein (HBB). 21 DNA variants are known to cause it; 10 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Also known as: Beta-thalassemia
Genes linked to Beta thalassemia
HBB: Hemoglobin subunit beta
Beta-globin, one of the two major protein chains in adult hemoglobin. Hemoglobin uses these chains to transport oxygen from the lungs to tissues, and HBB variants are associated with sickle-cell disease and beta-thalassemia.
21 disease-causing and 10 uncertain variants in HBB are linked to Beta thalassemia.
Known disease-causing variants in Beta thalassemia
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| HBB M1K | 1 | Disease-causing (★★) | |
| HBB M1I | 1 | Disease-causing (★★) | |
| HBB H64N | 64 | Globin | Disease-causing (★★) |
| HBB H64R | 64 | Globin | Disease-causing (★★) |
| HBB H64Y | 64 | Globin | Disease-causing (★★) |
| HBB L111P | 111 | Globin | Disease-causing (★★) |
| HBB M1L | 1 | Disease-causing (★★) | |
| HBB R31G | 31 | Globin | Disease-causing (★★) |
| HBB G108D | 108 | Globin | Disease-causing (★★) |
| HBB N109K | 109 | Globin | Disease-causing (★★) |
| HBB V99M | 99 | Globin | Disease-causing (★★) |
| HBB H144R | 144 | Globin | Disease-causing (★★) |
| HBB N20S | 20 | Globin | Disease-causing (★★) |
| HBB F43L | 43 | Globin | Disease-causing (★) |
| HBB E7M | 7 | Globin | Disease-causing (★) |
| HBB E102Q | 102 | Globin | Disease-causing (★) |
| HBB L115M | 115 | Globin | Disease-causing (★) |
| HBB R31S | 31 | Globin | Disease-causing |
| HBB Y36C | 36 | Globin | Disease-causing |
| HBB S90N | 90 | Globin | Disease-causing |
| HBB Q128R | 128 | Globin | Disease-causing |
Which prediction tools work for Beta thalassemia
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- AlphaMissense: 78 out of 100
- CATVariant: 76 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 62 out of 100
- ESM1b (LLR): 61 out of 100
Same protein, different disease
- Erythrocytosis, familial, 6 is also caused by HBB variants; they fall in the same places as the Beta thalassemia variants (31 disease-causing).
- Beta-thalassemia HBB/LCRB is also caused by HBB variants; they fall in the same places as the Beta thalassemia variants (18 disease-causing).
- Heinz body anemia is also caused by HBB variants; they fall in the same places as the Beta thalassemia variants (12 disease-causing).
- Hemoglobinopathy is also caused by HBB variants; they fall partly in the same places as the Beta thalassemia variants (12 disease-causing).
- Dominant beta-thalassemia is also caused by HBB variants; they fall partly in the same places as the Beta thalassemia variants (11 disease-causing).
Diseases related to Beta thalassemia
- Erythrocytosis, familial, 6, also linked to HBB
- Malaria, also linked to HBB
- Heinz body anemia, also linked to HBB
- Atypical hemolytic-uremic syndrome, also linked to HBB
- Beta-thalassemia HBB/LCRB, also linked to HBB
- Hemoglobinopathy, also linked to HBB
- Dominant beta-thalassemia, also linked to HBB
- Alpha Thalassemia, also linked to HBB
- METHEMOGLOBINEMIA, BETA TYPE, also linked to HBB
- Hemolytic anemia, also linked to HBB
Frequently asked questions
Which genes are linked to Beta thalassemia?
In CATVariant, Beta thalassemia is linked to 1 analyzed protein: HBB (Hemoglobin subunit beta).
How many genetic variants are linked to Beta thalassemia?
51 variants: 21 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 10 are of uncertain significance or have conflicting reports.
Which uncertain variants in Beta thalassemia look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
Which variant effect predictor works best for Beta thalassemia?
Among tools not trained on clinical labels, AlphaMissense separates this disease's known disease-causing variants from harmless ones best (AUROC 0.78, based on 21 disease-causing and 19 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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